I have 3 ideas here, all seem reasonable:
Idea 1)
There is a hardcoded, BB exception for certain historical annexations: for example, Spain annexing Grenada, but not for "non-historical" annexations, such as Prussia annexing Mysore. This may make sense, as Europe may have in some way supported the spanish aquisition of Grenada, etc... Thus, the BB rules are:
+1 for each SAME RELIGION province
+0 for each DIFFERENT RELIGION province
+3 and +1 per province for ANY military annexation regardless of religion
With certain "built in" BB exceptions, such as the Grenada annexation.
With this solution to the problem, everyone can be right...
Idea 2)
The "pagan" religion is treated differently in MANY respects: There is no religion slider for it, it always has a +1 revolt risk (modifiable) associated with it, perhaps the game is hardcoded to treat pagan states as same religion states for BB purposes only; while moslem/christian is treated as different religions. Thus, annexing grenada(moslem) invokes a different BB rule than annexing mysore(pagan)
Idea 3) Spain starts the game with a -5 BB rating. Thus with the annexation of grenada they move up to a +1 rating. Did anyone check the Spain BB rating BEFORE the annexation of Grenada?